BTW, while I'm here, is "I" capitalized in the middle of a sentence (e.g. "I think I should go")? I don't know where I got that from: maybe I made it up...
As long as "I" refers to the first person, it is always capitalized, no matter where it appears in a sentence.
"I think I should go, shouldn't I?"
Some authors will do that gender-balance thing, but I see it more in non-scientific writing, or perhaps writing about a technical subject that is aimed at a non-technical audience.
If I were writing a technical article, I'd write something like "when typing the command -foo-, the user expects output -bar-". Or "when they type the command -foo-, users expect output -bar-". If my audience were non-technical, I might write "when you type the command -foo-, you expect output -bar-". Another possibility is "when he/she types the command -foo-, the user expects output -bar-".
All of those are a bit awkward sounding, however, and it has nothing to do with gender. I'd prefer to put the noun first and the pronoun second, and I'd add a the in front of "output.".
"when the user types the command -foo-, she expects the output -bar-".
"when users types the command -foo-, they expect the output -bar-".
"when the user types the command -foo-, he/she expects the output -bar-".